|
| Status |
Public on Dec 15, 2022 |
| Title |
277-LN: Lymph Node Of AITL-Carrying NSG Mouse #277 |
| Sample type |
SRA |
| |
|
| Source name |
Lymph Node
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: Angioimmunoblastic T-cell Lymphoma Xenograft
treatment: CXCR5-antagonist
mouse strain: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG)
xenograft number: DFTL-78024
|
| Treatment protocol |
Mice were treated twice daily by oral gavage at 40mg/kg of compound with 4.7% DMSO in PBS as the vehicle or an equivalent volume of vehicle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lymph nodes were excised and formalin-fixed/paraffin-embedded. Slices of tissue were deparaffinized and rRNA was depleted.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were filtered for quality and aligned to hg38 with Ensembl Transcripts release 100 and mm10 with Ensembl Transcripts release 100 using Partek Flow (v10.0.21.0509)
Aligned reads were separated into mouse and human reads using XenofilteR v1.6
Reads were then quantified and analyzed again with Partek Flow. Transcripts with £10 reads were removed and separated aligned reads were normalized to the total number of counts per sample.
Transcripts were used for Gene Specific Analysis and Alternative Splicing Detection using Partek Flow (v10.0.21.0509)
Genome_build: hg38, mm10
Supplementary_files_format_and_content: csv files containing the differential gene expressions, fold change, p-values, and corrected p-values
Supplementary_files_format_and_content: tab-delimited txt files containing the differential splice variant expressions, fold change, p-values, and corrected p-values
Supplementary_files_format_and_content: Filtered BED files containig human-only and mouse-only transcripts.
|
| |
|
| Submission date |
Dec 17, 2021 |
| Last update date |
Dec 17, 2022 |
| Contact name |
Elias Lolis |
| Organization name |
Yale University
|
| Department |
Pharmacology
|
| Street address |
PO Box 208066, 333 Cedar St.
|
| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06520 |
| Country |
USA |
| |
|
| Platform ID |
GPL25431 |
| Series (1) |
| GSE191119 |
CXCR5 Antagonist in Angioimmunoblastic T-cell Lymphoma |
|
| Relations |
| BioSample |
SAMN24167161 |
| SRA |
SRX13437451 |
